Microbiome Teams Up Against C. diff

Researchers build a mathematical model that can predict whether a mouse will be infected by Clostridium difficilebased on the microbes found in its GI tract.

By Jef Akst | July 14, 2015

Clostridium difficile WIKIMEDIA, BOTGut bacteria are critical in fighting Clostridium difficile, highlighted by the recent successes in using fecal transplants in treating such infections. But resistance to C. diff infections can’t be attributed to any one microbe; rather, it’s the community of bacteria in the gut that matter, according to a new study that modeled the incidence of infection in mice based on their microbiota.

Patrick Schloss, a microbiologist at the University of Michigan in Ann Arbor, and his colleagues started by giving mice various antibiotics to see how the treatments affected the composition of bacteria in their guts. Then, the researchers challenged the mice with C. difficile and built a mathematical model that could predict a mouse’s susceptibility to the pathogen with 90-percent accuracy. They published their results today (July 14) in mBio.

Bacteria belonging to certain groups, such as Porphyromonadaceae, Lachnospiraceae, Lactobacillus, Alistipes, and Turicibacter, appeared to protect the mice against C. difficile. Loss of those species correlated with an increase in susceptibility, as did an increase in Escherichia or Streptococcus bacteria. “Susceptibility is not all or nothing—it’s extremely context dependent,” Schloss said in a press release. “I think about it as a buffet, where you have to mix and match different ingredients to get resistance or sensitivity to C. difficile.”

The researchers note that if a predictive model of this kind could be constructed for humans’ susceptibility to C. difficile, it could help prevent hospital patients from becoming infected. “If we could assess a patient’s microbiota from a stool sample—especially if they are getting antibiotics—we could look at what bacteria are missing,” coauthor Alyxandria Schubert, a postdoc in Schloss’s lab, said in the release. “You could perhaps give patients a probiotic supplement with the goal of restoring their microbiota community structure to a healthy state.”